It never runs smooth
by Yvy
Summary: What if Bones and Booth had been together all along & had a child? Last chapter up.
1. She is coming home

**I don't own Bones.**

**What if Bones and Booth had been together all along? What if they had child together? Slightly AU and by slight I mean completely. **

**Little back-story: Bones and Booth were in love but silly them they kept it well hidden. Booth had a hit out on him, Bones got pregnant. They were forced to take their baby to live with Jared- Booth's brother until it is safe enough to bring baby home. That time is now. I know there are some inconsistencies but this has been running round my head for a while. Enjoy.**

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"Hey! Cam have you seen Bones?" Asked flustered Booth, who was clutching a cup of coffee in his shaking hand. "Man, I'm out of breath."

Cam turned around and walked up to, her impossibly high heels clopping loudly on the cold, hard floor. She nodded her head and motioned to the bone room.

"She's in there, talking to the head of the department. You shall have to wait."

Booth let out a groan of annoyance. "It can't wait."

"Well, Booth." Cam said, smiling slightly at the special agent, who was hopping impatiently from foot to foot. "Tough. She should be done soon."

"How soon is soon?"

"I don't know! So is it some grizzly murder you need her for?" Cam asked curiously, Brennan seemed to spending less and less time in the lab of late and to be honest Dr Saroyan didn't mind- the murder still got solved and she got rid of one Dr, one Dr who, obviously, didn't like her acting superior.

"No, that hit on my head is gone- FBI cracked the circle and now Mr "I have twelve guns and a fast car" is spending his days in a jail. Far away."

"Oh?"

Booth grinned from ear to ear, he finally felt free to be able to bring his baby home, to love Bones without fear of her being shot, killed or fed to a dog. Life was finally looking up. He couldn't wait to introduce Parker to his little sister. Or to see the look on his Bones' face when he told her the news. He couldn't wait.

"Excuse me Camille."

He barged past the woman, sprinting down the hall until he got to the room. The door was shut, he half expected a do-not-disturb sign to be hung up- those scientists got funny about their privacy. Copper hair flung round as he burst into the room. He saw Bones' eyes widen, the department guy looked shock at Booth's behaviour.

"Booth?" Brennan hissed. "What are you doing here? Can't you see I'm in an important meeting?"

The other man was staring daggers at Booth. He was fed up of the bureau rushing in and taking his best scientist.

"Yeah well Bones- this is important."

"So is this!"

Booth moved closer, grinning at Bones. "This is better, trust me."

"Excuse me one second." Brennan said as politely as she could to her colleague and pulled Booth roughly to the side.

"It's over Bones. Trebuchet was arrested. The hit's over. Emilia can come home."

Bones smiled and looked at the department head, grimacing she excused herself and her partner and dragged him outside. Tears were collecting in her eyes. It was over.

"When? When do we get her back? Can we go? Get Emi, I mean?"

Booth gripped her shoulders tightly and pulled her into a hug, whispering in his ear how much he did, honestly, love her.

"We can go as soon as we're ready. Up to Jared's and back with Emi. Is that alright?"

Booth felt Bones groan into his shoulder. Her hair tiled his neck as he looked down into her pale, blue eyes.

"What is it?"

"I said I'd help Zack identify some Inuit remains for an exhibit tomorrow. I can't just abandon him."

Booth rested his chin in Bones' head as he began to think. Even if they did go get their daughter today, they had nothing for her- no bed, no food, not toys. However if they went to tomorrow then they had today to prepare everything, to be able to give their beautiful daughter a proper home.

"Then it is settled." Bones said when they had discussed what to do. They would go tomorrow, having beforehand decked out Brennan's apartment with baby "stuff".

"Booth?"

"Yeah Babe?"

"Is she really coming home?"

Booth nodded as he pulled the love of his life in for a kiss.

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**Did you like? Chapter 2 should be up soon. And it will involve the reactions of the squints to the news that their favourite non-couple actually have a baby. Please let me know if there are any major things wrong. Also- Sully didn't happen and neither did Cam and Booth- just so you know.**

**Hit the pretty button please.**


	2. Who ordered a baby?

"Hey, Hodgins have you seen Brennan? Or Booth, for that matter?"

"Well, I think Booth said something very important had come up, then they rushed of together. "

"The path of true love never runs smooth."

They exchanged glances and smiled. Angela walked up to Hodgins and pecked him on the cheek. Zack shook his head that pair and went back to correcting a paper.

The group minus Booth and Brennan of course were sat above the lab, going over previous paperwork that they had to fill out. All was silent apart from the furious clicking of a broken, clicky pen that Zack was frowning at.

"My pen is broken and there is a naked lady on it."

Cam chuckled to herself. "That would be Booth's then."

She looked out across her domain- it all looked fairly clean today, suddenly her eyes fell on a girl clutching a baby who was wandering up to the steps. Cam frowned and turned quickly to her group.

"Who ordered a baby?"

"A baby?" Asked Angela, a furrow forming between her perfectly shaped brow- she was looking extremely confused.

"What?" Hodgins leant over the sidebar and looked down to see a blonde girl flick her head up and smile shyly at them. The baby in her arms moved and out a small squeak.

"Hi. Have you seen Seeley Booth? I was meant to be dropping this one off for him." The blonde girl who couldn't have been more that nineteen stood beneath them rocking slightly and string up at four bemused faces.

"Is the baby Booth's?" Angela asked Cam. Cam shook her head.

"I have no idea- but she looks a bit young don't you think?"

"I agree." Whispered Hodgins, conscious not to let the girl overhear.

Angela suddenly sprang into action and ran down the stairs to the girl

"Hi, I'm Angela. And you are?"

"Caitlin- Seeley's niece."

"His niece?" Angela faltered trying not to gag. Booth had a baby with his niece? Something was not right there. "And is this your baby?"

"Oh God no! Eww. No. This is Emi; she's just been living with me and my mom and ad whilst Seeley's been having the whole death thing going on." Caitlin explained fast, tumbling over the words. She was nervous.

"Well. Well! So is a certain Temperance Brennan this beautiful baby's mommy? It's so gotta be her. I mean come on, there's no one else who Booth would have kid with is there?"

Angela looked up at Hodgins, Zack and Cam- none of the three had moved since she had ran down the stairs to greet the perplexing visitor. Cam fleetingly remembered that she now owed Angela twelve dollars, the bet being Bones and Booth would have had a kid before Zack got a girlfriend.

Caitlin grinned and shook her head at Angela.

"It could be no one else." She paused and looked nervously around. "So anywho, is Seeley nearby? Or am I going to have to wait here? With the bones? It's a bit creepy isn't it?"

Angela smiled to herself. Maybe she should move the girl to a nicer part of the building.

"He went out. Did he know you were coming?"

"I dunno- dad said he'd call him. Damn it."

Angela realised she was beginning to get a headache; she had absorbed a lot of surprising information in the past three minutes. She felt elated, happy and decidedly broody. Staring at the sleeping baby curled tightly up, wrapped in a Winnie-the-pooh sleep suit, she thought to herself._ I want one. _

"Well, wait here and we'll contact Booth for you." Hodgins said, he had managed to regain his battered senses, trotted down to the lab and put his arm around Angela.

"Thanks."

An uncomfortable silence filled the room; no one knew what to say. Shock. That was what everyone seemed to be feeling. _Brennan and Booth?__ They had hid that one well. _

Zack was still confused- wondering how you could keep a baby a secret. They're too loud.

Suddenly there was a clattering and two indistinct voices of two people arguing at the far end of the room. Four heads whipped around to see a dishevelled Brennan and Booth walk into the room.

"Bones we're going to have to tell them." Booth said impatiently, completely unaware of the faces staring at them.

"No we won't." Brennan said quietly, indicating the Squints, niece and baby up ahead. Booth jerked his head up and grinned. Pulling Bones along by the hand they bounded up to the group, laughing quietly, Booth ushered the sleeping form into his arms.

"Hey baby."

"Alright, you two have some explaining to do." Muttered Hodgins, whilst secretly smiling at the sight before him.

**What will happen in Chapter 3? - T****hey do explain.**** Eugh.**


	3. Going home

Chapter 3.

Once there had been a small fuss over Emi, once Hodgins had forced Angela to sit down, have a drink of water and take extremely, deep breaths and after Caitlin had departed, four sets of eager eyes looked to the partners for answers.

"Um, well how to begin." Booth mused to himself, the baby asleep in his lap.

"At the beginning would be helpful Booth." Interjected Brennan.

"Alright. Err. Bones and I have been together for a few years and with the whole bounty on my head we decided to it was better to protect Em and have her live with my brother until it was safe."

"But when, exactly did Brennan have a baby?" Asked Angela, who was glaring at Brennan. This was a big secret to keep from someone who was supposedly her best friend.

"The six months I spent in Croatia, I wasn't in Croatia- I was in California waiting for the baby. Then she came and I came back here."

"So that's it. I think. If you have any more questions well they shall have to wait. Bones and I are going home to spend some time with our daughter."

"Doctor Saroyan, I can make up the time at the weekend if you want?" Queried a flustered Brennan, who was being ushered from the room by Booth.

"Just go Doctor Brennan." Was the reply.

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Sorry it was short. I have absolutely no idea what to do now with this story. Seriously. Ideas would be most appreciated. 


	4. Parker and a blue cot

Part 4

"So what now?" Asked Bones. She was attempting to bounce a happy looking baby on her knee and was staring up at Booth, who trying desperately to make a crib without looking at the instructions.

_Typical alpha-male tendencies._

"Now, Bones. We play happy families for a while."

"What's that?"

Booth didn't answer- he was too engrossed in attaching a phantom part of wood, which did not seem to belong on anywhere on the faded blue, _god-damned _crib.

"Want some help?"

Booth let out a moan and a frustrated no. He would finish this by himself even if it killed him. The baby yawned and he smiled up at his small family, however it was not complete _quite _yet. He had arranged for Parker and Rebecca to come over later in the day so that his son could finally meet his little sister. He was also dreading Rebecca's reaction to being kept in the dark about something so important to her son.

"Booth, Booth, Booth?"

He ignored Bones, who had placed Emilia down and had wandered off to find the manual. She was now standing in front of him, absently stroking at her daughters hair and waving her hand about like a lunatic.

Pointing down at the mass of blue wood and nails, she stated from the instructions: Extra parts included.

"You don't actually need that bit, Booth." She smiled down laughing at her determined and stubborn partner, hastily picking up her child as he cursed heavily under his breath- at least with Parker, Rebecca had insisted on buying a ready-made cot.

A couple of hours later, Booth was pacing in front of the cot, hurriedly put up in Booth's front room – they had made a decision to keep both apartments until they settled everything out. Booth's would be where they were a family and Bones' somewhere to catch up on sleep if they had an early day the next day.

However, Booth had also made a rule that Bones was not allowed to spend all her time working. She would have to learn to prioritise. They both would.

"Booth, you're pacing."

"Yeah well, what if Parker doesn't like Emi?"

"Of course he will, they're siblings- there will be some sort of bond, and of course maybe a bit of jealously but Parker is a good kid Booth." Mused Bones.

Booth nodded at her. Those were the kind of comments that had made him fall in love with her when they had first started working together.

The buzzer bleeped. It was not meant to bleep- it was meant to buzz, hence the name. I am going to have to fix that, Booth thought to himself.

Booth opened the door beaming wildly at Rebecca and Parker; Parker ran in and hugged his dad, whilst Rebecca waited politely to be let in.

"Hi dad!"

"Hey Seeley, Dr Brennan." Rebecca noticed a nervous looking Bones hanging back behind her ex. She couldn't help but notice that the room was filled with an odd sort of tension.

"Hello."

"You said you had something to show Parker?"

Parker looked up at Booth with expectant eyes. _Maybe it's a cowboy hat, _Parker wondered. Booth smiled nervously and went down to eye level with his favourite son.

"Hey kid."

"Hi? So what is it?" Parker was impatient and jigging around on two feet.

"Well, you know Dr Brennan right?"

"Yes." He gave a small wave to her and she waved back.

"Good, well. Um Parker, you have sister."

Rebecca's eyes widened and she frowned down at Booth and over at Bones, desperately trying to figure this one out. She may not be as smart as the good Doctor, but by god, she would work this one out.

"No I don't silly." Parker laughed at Booth.

Brennan took this as the ideal time to go fetch Emi from her slumber. She returned a few minutes later, noticing that everyone was still in the same position she had been when she left.

Parker's little face lit up as he ran towards Bones.

"Is this is?" He asked pointed at the baby.

"Yeah, Parker meet your new little sister."

"She is funny looking."

"She's a baby, her skeleton has not fully developed yet and her skull has yet to fall into place." Brennan said trying to make it so the boy could understand.

"Yeah you looked like this once, Parker." Booth said.

"What's her name?" Rebecca squeaked out, raising her eyebrows at Parker.

"Emi."

"Emi?" Rebecca queried, she had meant the full name, surname, silently wondering about the arguments that must have ensued when discussing whose last name _Emi_ would take. She remember them well.

Booth understood what she meant and elaborated.

"Emilia Christine Brennan-Booth. Bones didn't want to forget about her last name. "Parker reached out and poked his sister in the head, gently, she giggled and Parker introduced himself to his new most interesting thing. He ignored the 'adult' conversation going on over his head.

"Booth, we discussed it and you were perfectly happy with it, in the end and besides, I did all the work so suck it up." Booth grinned at her and rose to kiss her on the cheek.

"What does 'suck it up' mean mummy?" Parker asked, curiosity momentarily bringing his attention away from the baby. Rebecca ignored him and just stared at the two partners a look of confusion spreading further across her face.

"Seeley, Temperance?" Both women cringed at that, they weren't friendly enough for first names and they both knew it. "Dr Brennan, I have one question."

She paused, probably trying to work out how to phrase her question or possibly for dramatic effect.

"When the hell did you have a baby?"

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**What was the consensus on this part?**

**I am having so much trouble making these guys stay true to form. :(**


	5. Symmetrical features

**Squints'** **reactions then back on to Rebecca's "When the hell?".**

** Sorry about all the scene dividers or 'horizontal rulers' what ever you want to call them- but they are all there for a purpose so I hope they don't cause too much frustration.**

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Angela & Hodgins' reactions:

The day has started out pretty well, Hodgins had made her breakfast- raspberry pancakes- they had been nice; there were no fresh bodies for her to "face-up" and the sun was shining. Then Brennan comes along and drops a gigantic...

Huge...

Enormous...

Positively unbelievable bombshell on her.

Brennan and Booth have a kid- she may be cute, yeah whatever, but Angela was annoyed. Her best friend of _many_ years didn't even think that she was worth telling- or maybe it was that Brennan didn't think that Angela would be able to keep it a secret- not that that was any better that the first reason.

_How did I not tell she was pregnant? I'm usually so good at stuff like that!_

And yes, Angela had to admit- it had made her feel rather faint to find out the two she had been rooting for all along had "hit that" years before, she was now just slightly angry at them. This was probably very illogical. But who gives a damn about logic when something like this happens?

Hodgins looked bored as Angela relayed all her thoughts to him, his mind was drifting- somehow he wasn't _quite _so shocked as his fiancée about the day's developments. He only tuned back in when he heard Angela's final comment.

"I want a baby."

He coughed into his coffee and looked up.

"What? Now?"

"Yes." Replied Angela nonchalantly, with an extremely obvious raise of her perfectly preened eyebrows.

Gulping down his drink, he grabbed her hand and they made a run for the store cupboard.

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Cam's reaction:

Cam was not surprised, not in the slightest- it did explain why, in her first year of joining the Jeffersonian, Booth had been so good at avoiding her and her 'advances'. He was very sneaky. As for Dr Brennan- she was a very, very good actress. Cam remembered the few times Brennan had rushed to the loos, only to appear again several minutes later as white as a sheet.

"_I must have eaten some bad sushi."_

Yeah, bad sushi her ass.

The only consolation was that Brennan must have become quite big- unfortunately, she was in Croatia at that sad time- apparently, but the fact remained Brennan would have missed her toes. Cam had always been slightly jealous at what appeared to be Brennan's effortlessly- kept figure. Not anymore.

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Zackaroni's reaction:

Dr Brennan had a baby- and from the look of it, Booth's and her genes worked well together. They were obviously both good breeders, symmetrical features a good indication of that and then there was always sexual tension. Basically, Zack should have know that something was going on, he was a trained anthropologist- meaning people. He may not be very good himself with people but he should have noticed this.

Another thing, if Brennan had been pregnant her pelvic girdle would have begun shifting to get ready for childbirth, the bones loosen- it's quite a radical shift, so why didn't he notice it? Or maybe he had and didn't say anything, he must have thought the probability of Brennan being pregnant, to be extremely low. Apparently not.

The scientist in him should have noticed something, anything. Thus Zack came to the conclusion that he was not a good a scientist as he thought. His next thought was he needed to study more, perhaps do some intense research into pregnant women and how easy it is to recognise it early on. That way he would not miss it if something like this happened again.

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Meanwhile back in Booth's apartment...

"_When the hell did you have a baby?"_

Apparently questioning the parentage of was not an issue to Rebecca- in her mind there were only two candidates, both of whom were standing in front of her.

"Croatia." Brennan said, as if it explained everything.

"Croatia?" Echoed Rebecca, the furrow between her brow getting even deeper.

"I wasn't in Croatia for the whole time I said I was- half the time I was being pregnant. Then giving birth, then a few months with Emilia. Quietly of course, because someone had decided to put a hit out for Booth. Plus I didn't get _that _big whilst I was pregnant."

Rebecca still looked confused, Booth ushered her to sit down , hurriedly clearing a dummy, several pairs of socks and a blanket off his sofa. Booth started patiently to explain it all to Rebecca- perhaps more clearly that Bones' attempt.

"You know about the 'hit' on me right? Why I haven't been able to see Parker as much? If I pi..." Booth checked himself: _use a word suitable for baby ears Booth. _Deviating slightly from the her original question he also explained why now it was safe for Emilia to be back.

"If I _annoyed _a certain bunch of nasty men off then BAM! I err, get shot in the head. But the guy who set that up has now been arrested ." He said with a smile and a glance over at Brennan who was watching Parker introduce himself to his sister.

"Seeley? Are you going to continue?" Rebecca asked.

"Well yeah, when Bones got pregnant we agreed to keep it secret- to protect the baby, Bones and myself. Bones still went on her little jaunt to Croatia for a few months but that was cut short by the whole '_having _the baby' thing. Then Emi went to live with Jared for a while when she was born- until we figured out what to do next."

They sat in silence as slowly Rebecca's eyes shrunk back to their normal size and she smiled.

"Have I already said congratulations?" She hugged Booth and then Brennan- who wasn't as immune to social ways as Rebecca had first thought. "So I guess you two did catch fire then?"

"Fire's bad- I learned that at school." Piped-up Parker, very matter-of-factly. He seemed to be trying to teach the baby to play pat-a-cake. It was not working.

"I'm hungry."

"Want to go get something to eat Parker?"

He nodded.

"Well mommy needs a drink-a very stiff drink. I suggest we all go somewhere."

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**4 days! 4 days 'till Bones is back. In the UK I mean, although I've spoilered the episodes already- whoops. **

**How impatient...**


	6. L'avenir

**This is set years into the future. Last Chapter.**

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"So I spent the first few months of my life living with uncle Jared because some mafia style guy wanted to kill you?" A fifteen-year-old Emilia, teased her parents about her baby years constantly. It got her sympathy points occasionally, if she felt daddy was 'neglecting' her. Neglect being if they missed their weekly ice cream and movie deal. It got her hugs from her mother too, especially at Christmas.

"And you've been what? Buried alive, blown up... by a fridge _and_ by a bag-bomb full of teeth. You shot a clown, have been almost eaten and almost killed-copious amounts of times. Oh also I forgot! No one knew I existed for over a year. And do I even need to mention voodoo amnesia?"

Bones and Booth laughed at their daughter, she found their past extremely amusing. When she was little instead of fairy stories about girls with long blonde hair and glass slippers, it was fantastic adventures about serial killers and Thai food. It may have seemed odd to tell a two year old about serial killers with face eating habits- but Brennan had found it was the only thing that got Emi to sleep.

"But hey, everything turned out alright in the end." Booth said, with grin at his Bones.

"Hell yeah. Your jobs sound _so_cool!" Emi smiled at their shocked looks, they didn't want their eldest daughter being in the face of death every other day. "But lucky for you I wanna be an art teacher."

She walked out of the front room of their DC apartment, to look for Parker, who occasionally used Booth's house as a base- when he was visiting. So when he came, Parker bunked in Emi's room. They stayed up late watching old silent films and in Brennan's eyes 'anthropologically speaking'; they were the epitome of a good brother and sister.

They looked alike; Parker an ash-blonde, curly haired version of his father and whilst Emi had her mother's stubborn jaw, they had both inherited Booth's dark eyes. In the right light, Emilia looked a lot like Brennan's mother, the likeness growing ever stronger as she grew up.

"Thank God." Booth said as he leant back against his chair, raising his eyebrows at Bones.

"She would have made a good anthropologist." Brennan said, slightly upset that Emi had rejected Brennan's favourite vocation.

"We'll leave the bones to you, Bones. We're not all super geniuses, or is it Geniii?" He mused.

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**Well it's over- sorry this chapter is short, but I didn't know how to end it. I just knew it needed ending. I know I didn't put in any of Max's reaction but basically it would have been: Sob, sob my daughter all grown up, she's so cute, I'm a grandpa. Happy happy. Then Booth would have reminded him he was in jail and the mood would have been deflated. **


End file.
